Understanding the genetic regulation of circulating protein levels can provide new insights into disease mechanisms. Here, we present the largest proteogenomic study to date (n = 78,664 participants across 38 studies), identifying >24,000 protein quantitative trait loci (QTLs) associated with 1,116 proteins, acting near to (n = 5,040) or distant (n = 19,698) from the cognate gene. Using machine learning-guided effector gene assignment, we provide genetic evidence for pathways, cell types, and tissues that modulate circulating protein levels, highlighting N-linked glycosylation as an important regulatory pathway. We demonstrate that genetic instruments of protein production/function ("cis") versus modulation ("trans") reveal distinct phenotypic insights. We identify proteins as candidates for drug targets and engagement (e.g., plasma furin and cardiovascular diseases) by comparing cis-based genetic evidence with protein-disease associations. Systematic triangulation of trans-protein QTLs (pQTLs) with genetic and protein associations across many diseases highlights potential drug repurposing opportunities, e.g., tyrosine kinase 2 (TYK2) inhibitors for rheumatoid arthritis. Our multi-cohort meta-analyses generate proteogenomic insights into disease mechanisms and new treatment opportunities.
Institut(e)Institute of Epidemiology (EPI) Institute of Translational Genomics (ITG)
FörderungenGates Cambridge Trust Sir Henry Dale Fellowship - Royal Society Estonian Research Council European Commission Swedish Research Council Novo Nordisk Foundation Vinnova Swedish Foundation for Strategic Research (LUDC-IRC) Exodiab European Research Council (ERC) Dutch Research Council (NWO) VICI Dutch Research Council (NWO) KIC Stichting Ammodo Dutch Heart Foundation Department of Veterans Affairs Sir Henry Dale Fellowship - Wellcome Trust German Centre for Cardiovascular Research (DZHK) Cancer Research UK UKRI Nuffield Department of Population Health (NDPH) MRC Swedish Research Council (Vetenskapsradet) Swedish Heart Lung Foundation (Hjart-Lungfonden) British Heart Foundation (BHF) National Institutes of Health (NIH) MRC Human Genetics Unit program (QTL in Health and Disease) Qatar National Research Fund ReumaNL Netherlands Organization for Scientific Research NWO-VICI NWO Gravitation grant ExposomeNL NWO KIC ZonMW ME/CFS EU Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Science (CIFMS), China European Union (ERC) DZHK (German Centre for Cardiovascular Research) site Berlin Biomedical Research Program at WCMQ - Qatar Foundation Knut and Alice Wallenberg Foundation European Academy of Allergy and Clinical Immunology (EAACI) European Respiratory Society (ERS) British Heart Foundation National Institute for Health and Care Research Oxford Biomedical Research Centre British Heart Foundation Oxford Centre of Research Excellence Nuffield Department of Population Health, University of Oxford, UK Swedish Heart Lung Foundation Brain Foundation RCUK Innovation Fellowship from the National Productivity Investment Fund Olle Engkvist Foundation for proteomics analyses National Key Research and Development Program National Natural Science Foundation of China (NSFC)